Variant 6-8361158-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.608 in 151,936 control chromosomes in the GnomAD database, including 29,020 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.61 ( 29020 hom., cov: 31)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.539

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.943 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.8361158A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	Effect
ENSG00000285216	ENST00000644718.1 linkuse as main transcript	n.560+53598A>G	intron_variant
ENSG00000234763	ENST00000651914.1 linkuse as main transcript	n.311+1562T>C	intron_variant
ENSG00000234763	ENST00000655767.1 linkuse as main transcript	n.341+1562T>C	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.608

AC:

92367

AN:

151816

Hom.:

29007

Cov.:

show subpopulations

Gnomad AFR

AF:

0.489

Gnomad AMI

AF:

0.605

Gnomad AMR

AF:

0.675

Gnomad ASJ

AF:

0.593

Gnomad EAS

AF:

0.965

Gnomad SAS

AF:

0.717

Gnomad FIN

AF:

0.710

Gnomad MID

AF:

0.605

Gnomad NFE

AF:

0.617

Gnomad OTH

AF:

0.605

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.608

AC:

92410

AN:

151936

Hom.:

29020

Cov.:

AF XY:

0.619

AC XY:

45975

AN XY:

74230

show subpopulations

Gnomad4 AFR

AF:

0.488

Gnomad4 AMR

AF:

0.675

Gnomad4 ASJ

AF:

0.593

Gnomad4 EAS

AF:

0.965

Gnomad4 SAS

AF:

0.717

Gnomad4 FIN

AF:

0.710

Gnomad4 NFE

AF:

0.617

Gnomad4 OTH

AF:

0.610

Alfa

AF:

0.623

Hom.:

14883

Bravo

AF:

0.599

Asia WGS

AF:

0.830

AC:

2883

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

3.1

DANN

Benign

0.67

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over